{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T21:17:28Z","timestamp":1792790248008,"version":"4.5.0"},"reference-count":92,"publisher":"Korean Society of Animal Science and Technology","issue":"3","license":[{"start":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T00:00:00Z","timestamp":1777593600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0"}],"funder":[{"name":"Agricultural Research Service","award":["5090-31000-024"],"award-info":[{"award-number":["5090-31000-024"]}],"id":[{"id":"https:\/\/ror.org\/02d2m2044","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Agricultural Research Service","award":["5090-31000-026"],"award-info":[{"award-number":["5090-31000-026"]}],"id":[{"id":"https:\/\/ror.org\/02d2m2044","id-type":"ROR","asserted-by":"crossref"}]},{"name":"Agricultural Research Service","award":["0500-00093-001-00-D"],"award-info":[{"award-number":["0500-00093-001-00-D"]}],"id":[{"id":"https:\/\/ror.org\/02d2m2044","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.ejast.org"],"crossmark-restriction":true},"short-container-title":["J Anim Sci Technol"],"published-print":{"date-parts":[[2026,5]]},"abstract":"<jats:p>Nutritional studies in the cattle typically focus on the rumen and its microbial\n                    environment, leaving other parts of the gastrointestinal (GI) tract largely\n                    unexplored. Thus, underlying molecular mechanisms and the responses to dietary\n                    treatment in the lower gut is poorly understood. In this study, we investigated\n                    the caecum transcriptome changes and its associated microbial communities in\n                    calves with or without artificially dosed rumen content extracted from an adult\n                    cow. Eight calves were included in the study, four received artificially dosed\n                    adult rumen content (Treated) and the rest received autoclaved rumen content as\n                    a control. We observed significant transcriptome changes in the caecum between\n                    treatments, with 1,836 differentially expressed genes (DEGs) identified. A\n                    predominant portion of the DEGs were down-regulated in the treated group, which\n                    showed significant enrichment for molecular pathways related to immune response,\n                    host response to pathogens, and inflammatory responses. For the DEGs correlated\n                    with the highest number of microbes, gene ontology analysis indicated an\n                    enrichment in pathways associated with inflammation and immune response. By\n                    comparing the microbial taxa abundance among different GI tissues collected from\n                    the same study, we observed that the same dosing strategy may lead to\n                    differential retention of the microbial community in different GI tract\n                    locations. Our work indicated that the hind gut showed robust response to\n                    artificial dosing and the caecum microbial community may interact extensively\n                    with the host to shape the development and maturity of the host immune system in\n                    early life. Furthermore, our analysis suggested that tissue-specific analysis is\n                    required to fully understand the impact of early dosing on animal performance\n                    and physiology.<\/jats:p>","DOI":"10.5187\/jast.2024.e27","type":"journal-article","created":{"date-parts":[[2024,3,21]],"date-time":"2024-03-21T05:10:38Z","timestamp":1710997838000},"page":"857-874","update-policy":"https:\/\/doi.org\/10.5187\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Caecum transcriptome and associated microbial community in young\n                    calves with artificial dosing of rumen content obtained from an adult\n                    cow"],"prefix":"10.5187","volume":"68","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9006-0634","authenticated-orcid":false,"given":"Wenli","family":"Li","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02d2m2044","id-type":"ROR","asserted-by":"publisher"}],"name":"US Dairy Forage Research Center, Agricultural Research Service, USDA, Madison, WI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0002-1762-6379","authenticated-orcid":false,"given":"Brianna","family":"Murphy","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/040vxhp34","id-type":"ROR","asserted-by":"publisher"}],"name":"Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA"},{"id":[{"id":"https:\/\/ror.org\/01y2jtd41","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6749-6133","authenticated-orcid":false,"given":"Anna","family":"Larsen","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/040vxhp34","id-type":"ROR","asserted-by":"publisher"}],"name":"Oak Ridge Institute for Science and Education, Oak Ridge, TN, USA"},{"id":[{"id":"https:\/\/ror.org\/01y2jtd41","id-type":"ROR","asserted-by":"publisher"}],"name":"Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"3132","published-online":{"date-parts":[[2026,5,31]]},"reference":[{"key":"key2.0261002113849e+13_B1","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1111\/jam.12405","article-title":"Establishment of ruminal bacterial community in dairy calves from\n                        birth to weaning is sequential","volume":"116","author":"Rey","year":"2014","journal-title":"J Appl Microbiol."},{"key":"key2.0261002113849e+13_B2","doi-asserted-by":"crossref","first-page":"490","DOI":"10.3390\/ani9080490","article-title":"Review of strategies to promote rumen development in\n                        calves","volume":"9","author":"Diao","year":"2019","journal-title":"Animals."},{"key":"key2.0261002113849e+13_B3","doi-asserted-by":"crossref","first-page":"272","DOI":"10.1111\/j.1574-6941.2010.00852.x","article-title":"The persistence of bacterial and methanogenic archaeal\n                        communities residing in the rumen of young lambs","volume":"72","author":"Y\u00e1\u00f1ez-Ruiz","year":"2010","journal-title":"FEMS Microbiol Ecol."},{"key":"key2.0261002113849e+13_B4","doi-asserted-by":"crossref","first-page":"48","DOI":"10.1016\/j.smallrumres.2015.05.015","article-title":"Programming rumen bacterial communities in newborn merino\n                        lambs","volume":"129","author":"de Barbieri","year":"2015","journal-title":"Small Rumin Res."},{"key":"key2.0261002113849e+13_B5","first-page":"E120","article-title":"Bacterial direct-fed microbials in ruminant diets: performance\n                        response and mode of action","volume":"81","author":"Krehbiel","year":"2003","journal-title":"J Anim Sci."},{"key":"key2.0261002113849e+13_B6","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1016\/j.femsre.2004.12.001","article-title":"The use of bacterial spore formers as probiotics","volume":"29","author":"Hong","year":"2005","journal-title":"FEMS Microbiol Rev."},{"key":"key2.0261002113849e+13_B7","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1017\/S0003356100007698","article-title":"Effect of Saccharomyces cerevisiae yeast culture supplement on\n                        ruminal metabolism in buffalo calves given a high concentrate\n                        diet","volume":"59","author":"Kumar","year":"1994","journal-title":"Anim Sci."},{"key":"key2.0261002113849e+13_B8","doi-asserted-by":"crossref","first-page":"5401","DOI":"10.3168\/jds.2015-10563","article-title":"Effects of Saccharomyces cerevisiae fermentation products on\n                        dairy calves: ruminal fermentation, gastrointestinal morphology, and\n                        microbial community","volume":"99","author":"Xiao","year":"2016","journal-title":"J Dairy Sci."},{"key":"key2.0261002113849e+13_B9","doi-asserted-by":"crossref","first-page":"1133","DOI":"10.3389\/fmicb.2015.01133","article-title":"Manipulating rumen microbiome and fermentation through\n                        interventions during early life: a review","volume":"6","author":"Y\u00e1\u00f1ez-Ruiz","year":"2015","journal-title":"Front Microbiol."},{"key":"key2.0261002113849e+13_B10","doi-asserted-by":"crossref","first-page":"4832","DOI":"10.2527\/jas.2012-6142","article-title":"Nutritional intervention in early life to manipulate rumen\n                        microbial colonization and methane output by kid goats\n                        postweaning","volume":"91","author":"Abecia","year":"2013","journal-title":"J Anim Sci."},{"key":"key2.0261002113849e+13_B11","doi-asserted-by":"crossref","first-page":"841463","DOI":"10.1155\/2014\/841463","article-title":"An antimethanogenic nutritional intervention in early life of\n                        ruminants modifies ruminal colonization by archaea","volume":"2014","author":"Abecia","year":"2014","journal-title":"Archaea."},{"key":"key2.0261002113849e+13_B12","doi-asserted-by":"crossref","first-page":"69","DOI":"10.1016\/j.imlet.2014.05.009","article-title":"Rumen transfaunation","volume":"162","author":"DePeters","year":"2014","journal-title":"Immunol Lett."},{"key":"key2.0261002113849e+13_B13","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1111\/jpn.13232","article-title":"Evaluation of the therapeutic efficacy of rumen\n                        transfaunation","volume":"104","author":"Steiner","year":"2020","journal-title":"J Anim Physiol Anim Nutr."},{"key":"key2.0261002113849e+13_B14","doi-asserted-by":"crossref","first-page":"915","DOI":"10.2460\/javma.2004.225.915","article-title":"Evaluation of rumen transfaunation after surgical correction of\n                        left-sided displacement of the abomasum in cows","volume":"225","author":"Rager","year":"2004","journal-title":"J Am Vet Med Assoc."},{"key":"key2.0261002113849e+13_B15","doi-asserted-by":"crossref","first-page":"154","DOI":"10.1016\/j.livsci.2013.12.021","article-title":"Effects of inoculation with rumen fluid on nutrient\n                        digestibility, growth performance and rumen fermentation of early weaned\n                        lambs","volume":"162","author":"Zhong","year":"2014","journal-title":"Livest Sci."},{"key":"key2.0261002113849e+13_B16","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1038\/s41598-018-37033-4","article-title":"Transcriptomics analysis of host liver and meta-transcriptome\n                        analysis of rumen epimural microbial community in young calves treated with\n                        artificial dosing of rumen content from adult donor cow","volume":"9","author":"Li","year":"2019","journal-title":"Sci Rep."},{"key":"key2.0261002113849e+13_B17","doi-asserted-by":"crossref","first-page":"424","DOI":"10.3390\/genes12030424","article-title":"The effects of artificially dosed adult rumen contents on\n                        abomasum transcriptome and associated microbial community structure in\n                        calves","volume":"12","author":"Gaowa","year":"2021","journal-title":"Genes."},{"key":"key2.0261002113849e+13_B18","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1152\/physiolgenomics.00005.2020","article-title":"Changes in the host transcriptome and microbial metatranscriptome\n                        of the ileum of dairy calves subjected to artificial dosing of exogenous\n                        rumen contents","volume":"52","author":"Li","year":"2020","journal-title":"Physiol Genomics."},{"key":"key2.0261002113849e+13_B19","doi-asserted-by":"crossref","first-page":"220","DOI":"10.1042\/bj0810220","article-title":"Effect of carbohydrates on the intestinal synthesis of thiamine\n                        in rats","volume":"81","author":"Nath","year":"1961","journal-title":"Biochem J."},{"key":"key2.0261002113849e+13_B20","doi-asserted-by":"crossref","first-page":"285","DOI":"10.1073\/pnas.28.7.285","article-title":"Synthesis of vitamins by intestinal bacteria","volume":"28","author":"Burkholder","year":"1942","journal-title":"Proc Natl Acad Sci USA."},{"key":"key2.0261002113849e+13_B21","doi-asserted-by":"crossref","first-page":"1120","DOI":"10.2527\/jas.2010-3460","article-title":"Ruminant nutrition symposium: productivity, digestion, and health\n                        responses to hindgut acidosis in ruminants","volume":"89","author":"Gressley","year":"2011","journal-title":"J Anim Sci."},{"key":"key2.0261002113849e+13_B22","doi-asserted-by":"crossref","first-page":"450","DOI":"10.2527\/jas1972.352450x","article-title":"Development of microbial activity in the alimentary tract of\n                        lambs","volume":"35","author":"Oh","year":"1972","journal-title":"J Anim Sci."},{"key":"key2.0261002113849e+13_B23","doi-asserted-by":"crossref","first-page":"476","DOI":"10.7591\/9781501732355","volume-title":"Nutritional ecology of the ruminant","author":"Van Soest","year":"1994","edition":"2nd ed"},{"key":"key2.0261002113849e+13_B24","doi-asserted-by":"crossref","first-page":"1727","DOI":"10.3390\/ani10101727","article-title":"Starch-rich diet induced rumen acidosis and hindgut dysbiosis in\n                        dairy cows of different lactations","volume":"10","author":"Neubauer","year":"2020","journal-title":"Animals."},{"key":"key2.0261002113849e+13_B25","doi-asserted-by":"crossref","first-page":"78","DOI":"10.1016\/j.anifeedsci.2006.01.019","article-title":"Production and metabolic effects of site of starch digestion in\n                        dairy cattle","volume":"130","author":"Reynolds","year":"2006","journal-title":"Anim Feed Sci Technol."},{"key":"key2.0261002113849e+13_B26","doi-asserted-by":"crossref","first-page":"5552","DOI":"10.3168\/jds.2007-0257","article-title":"Acidosis and lipopolysaccharide from Escherichia coli B:055 cause\n                        hyperpermeability of rumen and colon tissues","volume":"90","author":"Emmanuel","year":"2007","journal-title":"J Dairy Sci."},{"key":"key2.0261002113849e+13_B27","doi-asserted-by":"crossref","first-page":"937","DOI":"10.3389\/fmicb.2017.00937","article-title":"The structural and functional capacity of ruminal and cecal\n                        microbiota in growing cattle was unaffected by dietary supplementation of\n                        linseed oil and nitrate","volume":"8","author":"Popova","year":"2017","journal-title":"Front Microbiol."},{"key":"key2.0261002113849e+13_B28","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1038\/ismej.2011.131","article-title":"Comparative analyses of foregut and hindgut bacterial communities\n                        in hoatzins and cows","volume":"6","author":"Godoy-Vitorino","year":"2012","journal-title":"ISME J."},{"key":"key2.0261002113849e+13_B29","doi-asserted-by":"crossref","first-page":"485","DOI":"10.3168\/jds.S0022-0302(89)79130-X","article-title":"Production of volatile fatty acids in the rumen and cecum-colon\n                        of steers as affected by forage: concentrate and forage physical\n                        form","volume":"72","author":"Siciliano-jones","year":"1989","journal-title":"J Dairy Sci."},{"key":"key2.0261002113849e+13_B30","doi-asserted-by":"crossref","first-page":"4697","DOI":"10.1128\/AEM.00720-15","article-title":"Ruminal bacterial community composition in dairy cows is dynamic\n                        over the course of two lactations and correlates with feed\n                        efficiency","volume":"81","author":"Jewell","year":"2015","journal-title":"Appl Environ Microbiol."},{"key":"key2.0261002113849e+13_B31","doi-asserted-by":"crossref","first-page":"1687","DOI":"10.2527\/jas.2011-4528","article-title":"Triennial lactation symposium: opportunities for improving milk\n                        production efficiency in dairy cattle","volume":"90","author":"Connor","year":"2012","journal-title":"J Anim Sci."},{"key":"key2.0261002113849e+13_B32","volume-title":"Nutrient requirements of dairy cattle","author":"NRC (National Research Council)","year":"2001","edition":"7th rev. ed"},{"key":"key2.0261002113849e+13_B33","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1186\/s12859-016-0994-9","article-title":"Sample size calculation while controlling false discovery rate\n                        for differential expression analysis with RNA-sequencing\n                        experiments","volume":"17","author":"Bi","year":"2016","journal-title":"BMC Bioinformatics."},{"key":"key2.0261002113849e+13_B34","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1093\/bioinformatics\/bts635","article-title":"STAR: ultrafast universal RNA-seq aligner","volume":"29","author":"Dobin","year":"2013","journal-title":"Bioinformatics."},{"key":"key2.0261002113849e+13_B35","doi-asserted-by":"crossref","first-page":"550","DOI":"10.1186\/s13059-014-0550-8","article-title":"Moderated estimation of fold change and dispersion for RNA-seq\n                        data with DESeq2","volume":"15","author":"Love","year":"2014","journal-title":"Genome Biol."},{"key":"key2.0261002113849e+13_B36","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","article-title":"Controlling the false discovery rate: a practical and powerful\n                        approach to multiple testing","volume":"57","author":"Benjamini","year":"1995","journal-title":"J R Stat Soc B Series B Methodol."},{"key":"key2.0261002113849e+13_B37","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/nprot.2012.016","article-title":"Differential gene and transcript expression analysis of RNA-seq\n                        experiments with TopHat and Cufflinks","volume":"7","author":"Trapnell","year":"2012","journal-title":"Nat Protoc."},{"key":"key2.0261002113849e+13_B38","doi-asserted-by":"crossref","first-page":"1805","DOI":"10.1093\/bioinformatics\/bts251","article-title":"DAVID-WS: a stateful web service to facilitate gene\/protein list\n                        analysis","volume":"28","author":"Jiao","year":"2012","journal-title":"Bioinformatics."},{"key":"key2.0261002113849e+13_B39","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1083\/jcb.200111026","article-title":"The GTP binding proteins Gem and Rad are negative regulators of\n                        the Rho-Rho kinase pathway","volume":"157","author":"Ward","year":"2002","journal-title":"J Cell Biol."},{"key":"key2.0261002113849e+13_B40","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.3000310","article-title":"Lipoprotein receptor LRP1 regulates leptin signaling and energy\n                        homeostasis in the adult central nervous system","volume":"17","author":"Liu","year":"2019","journal-title":"PLOS Biol."},{"key":"key2.0261002113849e+13_B41","doi-asserted-by":"crossref","first-page":"1944","DOI":"10.1111\/1759-7714.13486","article-title":"High expression of KITLG is a new hallmark activating the MAPK\n                        pathway in type A and AB thymoma","volume":"11","author":"Yang","year":"2020","journal-title":"Thorac Cancer."},{"key":"key2.0261002113849e+13_B42","doi-asserted-by":"crossref","first-page":"1143","DOI":"10.1111\/j.1600-0854.2009.00935.x","article-title":"The calcium channel mucolipin-3 is a novel regulator of\n                        trafficking along the endosomal pathway","volume":"10","author":"Martina","year":"2009","journal-title":"Traffic."},{"key":"key2.0261002113849e+13_B43","doi-asserted-by":"crossref","first-page":"9826","DOI":"10.1074\/jbc.M110.169185","article-title":"Mucolipin-3 regulates luminal calcium, acidification, and\n                        membrane fusion in the endosomal pathway","volume":"286","author":"Lelouvier","year":"2011","journal-title":"J Biol Chem."},{"key":"key2.0261002113849e+13_B44","doi-asserted-by":"crossref","first-page":"735","DOI":"10.3389\/fendo.2019.00735","article-title":"Reduced expression of PLCXD3 associates with disruption of\n                        glucose sensing and insulin signaling in pancreatic\n                        \u03b2-cells","volume":"10","author":"Aljaibeji","year":"2019","journal-title":"Front Endocrinol."},{"key":"key2.0261002113849e+13_B45","doi-asserted-by":"crossref","first-page":"259","DOI":"10.1038\/s41589-018-0213-2","article-title":"IFITM3 directly engages and shuttles incoming virus particles to\n                        lysosomes","volume":"15","author":"Spence","year":"2019","journal-title":"Nat Chem Biol."},{"key":"key2.0261002113849e+13_B46","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0172674","article-title":"Selection of internal reference genes for normalization of\n                        reverse transcription quantitative polymerase chain reaction (RT-qPCR)\n                        analysis in the rumen epithelium","volume":"12","author":"Die","year":"2017","journal-title":"PLOS ONE."},{"key":"key2.0261002113849e+13_B47","doi-asserted-by":"crossref","first-page":"402","DOI":"10.1006\/meth.2001.1262","article-title":"Analysis of relative gene expression data using real-time\n                        quantitative PCR and the 2\u2212\u0394\u0394CT method","volume":"25","author":"Livak","year":"2001","journal-title":"Methods."},{"key":"key2.0261002113849e+13_B48","doi-asserted-by":"crossref","first-page":"3211","DOI":"10.1093\/bioinformatics\/bts611","article-title":"SortMeRNA: fast and accurate filtering of ribosomal RNAs in\n                        metatranscriptomic data","volume":"28","author":"Kopylova","year":"2012","journal-title":"Bioinformatics"},{"key":"key2.0261002113849e+13_B49","doi-asserted-by":"crossref","first-page":"R46","DOI":"10.1186\/gb-2014-15-3-r46","article-title":"Kraken: ultrafast metagenomic sequence classification using exact\n                        alignments","volume":"15","author":"Wood","year":"2014","journal-title":"Genome Biol."},{"key":"key2.0261002113849e+13_B50","doi-asserted-by":"crossref","first-page":"237","DOI":"10.3390\/v10050237","article-title":"The role of the polymeric immunoglobulin receptor and secretory\n                        immunoglobulins during mucosal infection and immunity","volume":"10","author":"Turula","year":"2018","journal-title":"Viruses."},{"key":"key2.0261002113849e+13_B51","doi-asserted-by":"crossref","first-page":"83","DOI":"10.1042\/bst0310083","article-title":"The role of Rap1 in integrin-mediated cell\n                        adhesion","volume":"31","author":"Bos","year":"2003","journal-title":"Biochem Soc Trans."},{"key":"key2.0261002113849e+13_B52","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1093\/emboj\/18.3.605","article-title":"The Rap1 GTPase functions as a regulator of morphogenesis in\n                        vivo","volume":"18","author":"Asha","year":"1999","journal-title":"EMBO J."},{"key":"key2.0261002113849e+13_B53","doi-asserted-by":"crossref","first-page":"1091","DOI":"10.1038\/nsmb.2905","article-title":"Structural determinants of integrin \u03b2-subunit specificity\n                        for latent TGF-\u03b2","volume":"21","author":"Dong","year":"2014","journal-title":"Nat Struct Mol Biol."},{"key":"key2.0261002113849e+13_B54","doi-asserted-by":"crossref","first-page":"7538","DOI":"10.1073\/pnas.88.17.7538","article-title":"Two-step model of leukocyte-endothelial cell interaction in\n                        inflammation: distinct roles for LECAM-1 and the leukocyte beta 2 integrins\n                        in vivo","volume":"88","author":"von Andrian","year":"1991","journal-title":"Proc Natl Acad Sci USA."},{"key":"key2.0261002113849e+13_B55","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1038\/nature06887","article-title":"Rapid leukocyte migration by integrin-independent flowing and\n                        squeezing","volume":"453","author":"L\u00e4mmermann","year":"2008","journal-title":"Nature."},{"key":"key2.0261002113849e+13_B56","doi-asserted-by":"crossref","first-page":"3704","DOI":"10.1038\/ncomms4704","article-title":"Generation of colonic IgA-secreting cells in the caecal\n                        patch","volume":"5","author":"Masahata","year":"2014","journal-title":"Nat Commun."},{"key":"key2.0261002113849e+13_B57","doi-asserted-by":"crossref","first-page":"1981","DOI":"10.1073\/pnas.0307317101","article-title":"Aberrant expansion of segmented filamentous bacteria in\n                        IgA-deficient gut","volume":"101","author":"Suzuki","year":"2004","journal-title":"Proc Natl Acad Sci USA."},{"key":"key2.0261002113849e+13_B58","doi-asserted-by":"crossref","first-page":"328","DOI":"10.1016\/j.chom.2007.09.013","article-title":"IgA response to symbiotic bacteria as a mediator of gut\n                        homeostasis","volume":"2","author":"Peterson","year":"2007","journal-title":"Cell Host Microbe."},{"key":"key2.0261002113849e+13_B59","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1038\/nrmicro2384","article-title":"The role of secretory antibodies in infection\n                        immunity","volume":"8","author":"Strugnell","year":"2010","journal-title":"Nat Rev Microbiol."},{"key":"key2.0261002113849e+13_B60","doi-asserted-by":"crossref","first-page":"4904","DOI":"10.1038\/s41598-022-08761-5","article-title":"Rumen and lower gut microbiomes relationship with feed efficiency\n                        and production traits throughout the lactation of Holstein dairy\n                        cows","volume":"12","author":"Monteiro","year":"2022","journal-title":"Sci Rep."},{"key":"key2.0261002113849e+13_B61","first-page":"3215","article-title":"Analysis of the gut bacterial communities in beef cattle and\n                        their association with feed intake, growth, and efficiency","volume":"95","author":"Myer","year":"2017","journal-title":"J Anim Sci."},{"key":"key2.0261002113849e+13_B62","doi-asserted-by":"crossref","first-page":"327","DOI":"10.2527\/jas.2015-9839","article-title":"Microbial community profiles of the jejunum from steers differing\n                        in feed efficiency","volume":"94","author":"Myer","year":"2016","journal-title":"J Anim Sci."},{"key":"key2.0261002113849e+13_B63","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1038\/nature07008","article-title":"A microbial symbiosis factor prevents intestinal inflammatory\n                        disease","volume":"453","author":"Mazmanian","year":"2008","journal-title":"Nature."},{"key":"key2.0261002113849e+13_B64","doi-asserted-by":"crossref","first-page":"337","DOI":"10.1126\/science.1198469","article-title":"Induction of colonic regulatory T cells by indigenous Clostridium\n                        species","volume":"331","author":"Atarashi","year":"2011","journal-title":"Science."},{"key":"key2.0261002113849e+13_B65","doi-asserted-by":"crossref","first-page":"eaaf9412","DOI":"10.1126\/scitranslmed.aaf9412","article-title":"Intestinal commensal bacteria mediate lung mucosal immunity and\n                        promote resistance of newborn mice to infection","volume":"9","author":"Gray","year":"2017","journal-title":"Sci Transl Med."},{"key":"key2.0261002113849e+13_B66","doi-asserted-by":"crossref","first-page":"2663","DOI":"10.3389\/fmicb.2017.02663","article-title":"Exogenous fecal microbiota transplantation from local adult pigs\n                        to crossbred newborn piglets","volume":"8","author":"Hu","year":"2018","journal-title":"Front Microbiol."},{"key":"key2.0261002113849e+13_B67","doi-asserted-by":"crossref","first-page":"R173","DOI":"10.1152\/ajpregu.00425.2004","article-title":"Functional organization of the bovine rumen\n                        epithelium","volume":"288","author":"Graham","year":"2005","journal-title":"Am J Physiol Regul Integr Comp Physiol."},{"key":"key2.0261002113849e+13_B68","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1186\/1757-4749-5-23","article-title":"Commensal Clostridia: leading players in the maintenance of gut\n                        homeostasis","volume":"5","author":"Lopetuso","year":"2013","journal-title":"Gut Pathog."},{"key":"key2.0261002113849e+13_B69","doi-asserted-by":"crossref","first-page":"1364","DOI":"10.1099\/mic.0.2007\/014621-0","article-title":"The lytic cassette of mycobacteriophage Ms6 encodes an enzyme\n                        with lipolytic activity","volume":"154","author":"Gil","year":"2008","journal-title":"Microbiology."},{"key":"key2.0261002113849e+13_B70","doi-asserted-by":"crossref","first-page":"1497","DOI":"10.1099\/mic.0.032821-0","article-title":"Mycobacteriophage Ms6 LysB specifically targets the outer\n                        membrane of Mycobacterium smegmatis","volume":"156","author":"Gil","year":"2010","journal-title":"Microbiology."},{"key":"key2.0261002113849e+13_B71","doi-asserted-by":"crossref","first-page":"1082","DOI":"10.1139\/g04-075","article-title":"Evolution of cow nonstomach lysozyme genes","volume":"47","author":"Irwin","year":"2004","journal-title":"Genome."},{"key":"key2.0261002113849e+13_B72","doi-asserted-by":"crossref","DOI":"10.1371\/journal.ppat.1006512","article-title":"From bacterial killing to immune modulation: recent insights into\n                        the functions of lysozyme","volume":"13","author":"Ragland","year":"2017","journal-title":"PLoS Pathog."},{"key":"key2.0261002113849e+13_B73","doi-asserted-by":"crossref","first-page":"568","DOI":"10.1093\/oxfordjournals.molbev.a025957","article-title":"Likelihood ratio tests for detecting positive selection and\n                        application to primate lysozyme evolution","volume":"15","author":"Yang","year":"1998","journal-title":"Mol Biol Evol."},{"key":"key2.0261002113849e+13_B74","doi-asserted-by":"crossref","first-page":"11387","DOI":"10.1016\/S0021-9258(18)60476-4","article-title":"Multiple cDNA sequences and the evolution of bovine stomach\n                        lysozyme","volume":"264","author":"Irwin","year":"1989","journal-title":"J Biol Chem."},{"key":"key2.0261002113849e+13_B75","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1186\/1472-6785-4-7","article-title":"Resistance of rumen bacteria murein to bovine gastric\n                        lysozyme","volume":"4","author":"Dom\u00ednguez-Bello","year":"2004","journal-title":"BMC Ecol."},{"key":"key2.0261002113849e+13_B76","doi-asserted-by":"crossref","first-page":"16116","DOI":"10.1038\/srep16116","article-title":"Characterising the bacterial microbiota across the\n                        gastrointestinal tracts of dairy cattle: membership and potential\n                        function","volume":"5","author":"Mao","year":"2015","journal-title":"Sci Rep."},{"key":"key2.0261002113849e+13_B77","doi-asserted-by":"crossref","first-page":"100","DOI":"10.5713\/ajas.16.0166","article-title":"Characterization of the microbial communities along the\n                        gastrointestinal tract of sheep by 454 pyrosequencing\n                        analysis","volume":"30","author":"Wang","year":"2017","journal-title":"Asian-Australas J Anim Sci."},{"key":"key2.0261002113849e+13_B78","first-page":"2585","article-title":"Feed efficiency phenotypes in lambs involve changes in ruminal,\n                        colonic, and small-intestine-located microbiota","volume":"95","author":"Perea","year":"2017","journal-title":"J Anim Sci."},{"key":"key2.0261002113849e+13_B79","doi-asserted-by":"crossref","first-page":"12257","DOI":"10.1038\/s41598-017-12481-6","article-title":"Metagenomic characterization of the effect of feed additives on\n                        the gut microbiome and antibiotic resistome of feedlot\n                        cattle","volume":"7","author":"Thomas","year":"2017","journal-title":"Sci Rep."},{"key":"key2.0261002113849e+13_B80","doi-asserted-by":"crossref","first-page":"32","DOI":"10.3389\/fmicb.2018.00032","article-title":"The dynamic distribution of small-tail Han sheep microbiota\n                        across different intestinal segments","volume":"9","author":"Zhang","year":"2018","journal-title":"Front Microbiol."},{"key":"key2.0261002113849e+13_B81","doi-asserted-by":"crossref","first-page":"9113","DOI":"10.1038\/s41598-020-66056-z","article-title":"The microbial biogeography of the gastrointestinal tract of\n                        preterm and term lambs","volume":"10","author":"Chong","year":"2020","journal-title":"Sci Rep."},{"key":"key2.0261002113849e+13_B82","doi-asserted-by":"crossref","first-page":"e00061","DOI":"10.1128\/AEM.00061-17","article-title":"Metatranscriptomic profiling reveals linkages between the active\n                        rumen microbiome and feed efficiency in beef cattle","volume":"83","author":"Li","year":"2017","journal-title":"Appl Environ Microbiol."},{"key":"key2.0261002113849e+13_B83","doi-asserted-by":"crossref","first-page":"e00970","DOI":"10.1128\/AEM.00970-18","article-title":"Assessment of rumen microbiota from a large dairy cattle cohort\n                        reveals the pan and core bacteriomes contributing to varied\n                        phenotypes","volume":"84","author":"Xue","year":"2018","journal-title":"Appl Environ Microbiol."},{"key":"key2.0261002113849e+13_B84","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1111\/j.1574-6968.2008.01343.x","article-title":"Linkage of microbial ecology to phenotype: correlation of rumen\n                        microbial ecology to cattle\u2019s feed efficiency","volume":"288","author":"Guan","year":"2008","journal-title":"FEMS Microbiol Lett."},{"key":"key2.0261002113849e+13_B85","doi-asserted-by":"crossref","first-page":"1203","DOI":"10.1128\/AEM.05114-11","article-title":"Impact of feed efficiency and diet on adaptive variations in the\n                        bacterial community in the rumen fluid of cattle","volume":"78","author":"Hernandez-Sanabria","year":"2012","journal-title":"Appl Environ Microbiol."},{"key":"key2.0261002113849e+13_B86","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0091864","article-title":"Relationship between the rumen microbiome and residual feed\n                        intake-efficiency of brahman bulls stocked on bermudagrass\n                        pastures","volume":"9","author":"McCann","year":"2014","journal-title":"PLOS ONE."},{"key":"key2.0261002113849e+13_B87","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0129174","article-title":"Rumen microbiome from steers differing in feed\n                        efficiency","volume":"10","author":"Myer","year":"2015","journal-title":"PLOS ONE."},{"key":"key2.0261002113849e+13_B88","doi-asserted-by":"crossref","first-page":"2958","DOI":"10.1038\/ismej.2016.62","article-title":"Specific microbiome-dependent mechanisms underlie the energy\n                        harvest efficiency of ruminants","volume":"10","author":"Shabat","year":"2016","journal-title":"ISME J."},{"key":"key2.0261002113849e+13_B89","doi-asserted-by":"crossref","first-page":"367","DOI":"10.3389\/fmicb.2020.00367","article-title":"Metatranscriptomic profiling reveals the effect of breed on\n                        active rumen eukaryotic composition in beef cattle with varied feed\n                        efficiency","volume":"11","author":"Zhang","year":"2020","journal-title":"Front Microbiol."},{"key":"key2.0261002113849e+13_B90","doi-asserted-by":"crossref","first-page":"1981","DOI":"10.3389\/fmicb.2020.01981","article-title":"Rumen microbiome composition is altered in sheep divergent in\n                        feed efficiency","volume":"11","author":"McLoughlin","year":"2020","journal-title":"Front Microbiol."},{"key":"key2.0261002113849e+13_B91","first-page":"186","article-title":"Various factors affecting microbial protein synthesis in the\n                        rumen","volume":"1","author":"Pathak","year":"2008","journal-title":"Vet World."},{"key":"key2.0261002113849e+13_B92","doi-asserted-by":"crossref","first-page":"157","DOI":"10.3390\/microorganisms9010157","article-title":"The effect of a high-grain diet on the rumen microbiome of goats\n                        with a special focus on anaerobic fungi","volume":"9","author":"Fliegerova","year":"2021","journal-title":"Microorganisms."}],"container-title":["Journal of Animal Science and Technology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/www.ejast.org\/download\/download_pdf?doi=10.5187\/jast.2024.e27","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/www.ejast.org\/download\/download_pdf?doi=10.5187\/jast.2024.e27","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T02:54:09Z","timestamp":1790909649000},"score":1,"resource":{"primary":{"URL":"http:\/\/www.ejast.org\/archive\/view_article?doi=10.5187\/jast.2024.e27"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5]]},"references-count":92,"journal-issue":{"issue":"3","published-online":{"date-parts":[[2026,5,31]]},"published-print":{"date-parts":[[2026,5]]}},"alternative-id":["10.5187\/jast.2024.e27"],"URL":"https:\/\/doi.org\/10.5187\/jast.2024.e27","relation":{},"ISSN":["2672-0191","2055-0391"],"issn-type":[{"value":"2672-0191","type":"print"},{"value":"2055-0391","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5]]},"assertion":[{"value":"2023-11-12","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-02-20","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}}]}}